asnS:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{|{{Prettytable}}
{|   id="H46a9bbe744804"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''asnS''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''asnS''
Asparagine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0921, b0930, JW0913, lcs, tss''<ref name='LIB:Riley_2006'/>, tss''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12419.H46a9bbe744804&page=12419&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0921, b0930, JW0913, lcs, tss''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='130457'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9bbe7bcf20"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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21.27 minutes&nbsp;
21.27 minutes&nbsp;
|
|
MG1655: 988208..986808<br />{{GBrowseFigureByCoord|985808|989208|ecoli|MG1655}}
MG1655: 988208..986808<br /><gbrowseImage>
name=NC_000913:986808..988208
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10094 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10094 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:985808..989208 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|985808|989208|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:986808..988208&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|986808|988208|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10094 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10094 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1006076..1004676<br /><gbrowseImage>
name=NC_012967:1004676..1006076
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1004676|1006076|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1004676|1006076|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 889776..891176<br /><gbrowseImage>
name=NC_012759:889776..891176
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|889776|891176|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|889776|891176|FASTA Dump}}
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|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 989407..988007<br />{{GBrowseFigureByCoord|987007|990407|ecoli_W3110|W3110}}  
W3110: 989407..988007<br /><gbrowseImage>
name=NC_007779:988007..989407
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|987007|990407|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|988007|989407|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 1042136..1040736<br /><gbrowseImage>
name=NC_010473:1040736..1042136
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:987007..990407 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1037936|1044936|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:988007..989407&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1037936|1044936|FASTA Dump}}
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
986811
|
Edman degradation
|
PMID:2693216<br />PMID:9298646<br />
|
 
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====Notes====
====Notes====
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-  
|
asnSP231L
|
 
|
P231L
|
Auxotrophies
|
(in temperature-sensitive mutant HO202)
|
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P0A8M0 UniProt:P0A8M0]
|-
|
asnSY426F
|
 
|
Y426F
|
Auxotrophies
|
No effect
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A8M0 UniProt:P0A8M0]
|-
|
asnSY426S
|
 
|
Y426S
|
Auxotrophies
|
15-fold increase in Km for ATP
|
 
|
|
&Delta;asnS (Keio:)
 
|
|
deletion
seeded from [http://www.uniprot.org/uniprot/P0A8M0 UniProt:P0A8M0]
|-
|
|
deletion
''asnS40''(ts)
|
|


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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
Auxotrophies
|
temperature sensitive
|
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[[cgscmutation:7220|CGSC:7220]]
|
|
   
   
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12419.A4e04b7daee577-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0913
JW0913
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGAAGCTGGCGTTACGCGGAGT  
Primer 2:CCGAAGCTGGCGTTACGCGGAGT  
|-
|-
|
[[:Category:Kohara_Phage:E1D1|E1D1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=218 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:11F5|11F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=219 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7F5|7F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=220 Genobase]
|
PMID:3038334
|-  
|
|
zca-1230::Tn10
zca-1230::Tn10
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CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zbj-1230::Tn10  
Synonyms:zbj-1230::Tn10  
|-
|-  
|
|
[[ycbS:Gene|zcb-3059::Tn10]]
[[ycbS:Gene|zcb-3059::Tn10]]
Line 206: Line 383:
|
|
est. P1 cotransduction: 58% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 58% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10094 EcoCyc:EG10094] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0092 EchoBASE:EB0092] 
EcoCyc:EG10094
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0930 EcoliGenExpDB:b0930] 
EcoGene:EG10094
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1072 ECOL199310CYC:C1072] 
RegulonDB:ECK120000090
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10094 EcoGene:EG10094]
[http://www.ncbi.nlm.nih.gov/gene?term=945555 GeneID:945555]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=ASNS ECOO157CYC:ASNS] 
EchoBASE:EB0092
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/993 CGSC:993] 
ASAP:ABE-0003162
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:asn genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 19 September 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

asnS

Mnemonic

Asparagine

Synonyms

ECK0921, b0930, JW0913, lcs, tss[1], tss

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

21.27 minutes 

MG1655: 988208..986808
<gbrowseImage> name=NC_000913:986808..988208 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1006076..1004676
<gbrowseImage> name=NC_012967:1004676..1006076 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 889776..891176
<gbrowseImage> name=NC_012759:889776..891176 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 989407..988007
<gbrowseImage> name=NC_007779:988007..989407 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1042136..1040736
<gbrowseImage> name=NC_010473:1040736..1042136 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

986811

Edman degradation

PMID:2693216[2]
PMID:9298646[3]


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

asnSP231L

P231L

Auxotrophies

(in temperature-sensitive mutant HO202)

Strain variation; seeded from UniProt:P0A8M0

asnSY426F

Y426F

Auxotrophies

No effect

seeded from UniProt:P0A8M0

asnSY426S

Y426S

Auxotrophies

15-fold increase in Km for ATP

seeded from UniProt:P0A8M0

asnS40(ts)

Auxotrophies

temperature sensitive

CGSC:7220


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0913

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAGCGTTGTGCCTGTAGCCGA

Primer 2:CCGAAGCTGGCGTTACGCGGAGT

E1D1

Kohara Phage

Genobase

PMID:3038334[5]

11F5

Kohara Phage

Genobase

PMID:3038334[5]

7F5

Kohara Phage

Genobase

PMID:3038334[5]

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[6]

est. P1 cotransduction: 18% [7]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[6]

est. P1 cotransduction: 58% [7]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10094

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10094

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000090

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945555

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0092

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003162

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Anselme, J & Härtlein, M (1989) Asparaginyl-tRNA synthetase from Escherichia coli has significant sequence homologies with yeast aspartyl-tRNA synthetase. Gene 84 481-5 PubMed
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  5. ↑ 5.0 5.1 5.2 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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